I think this might be a plot hole because if it had vanished, how the heck would she have been able to rule it?
Remember that it has been recently revealed that
Ponies are not necessarily born into royalty.
While not explicitly stated (that I can recall), it is implied that Princess Cadence (or Princess Mi Amore Cadenza) was not always a princess. At one point, she was Twilight Sparkle's babysitter (or foalsitter).
Previous to the reappearance of The Crystal Empire in season 3, it is never actually stated if - or where Princess Cadence and Shining Armor reign over.
Since The Crystal Empire had vanished for 1000 years, and it is very unlikely that Cadence is that old, there is little-to-no chance that Cadence even could have ruled over the Crystal Empire before it vanished.
As MLP Wikia explains:
Before the emergence of Nightmare Moon, the Crystal Empire was taken over by the evil unicorn, King Sombra, who turned it into a dark land and enslaved the crystal ponies. Princess Celestia and Princess Luna defeated him with their magic, turning him to shadow and imprisoning him in the ice of the arctic north, but not before he placed a curse on the Crystal Empire, causing it to vanish for a thousand years. After it returns, the Crystal Ponies have no memory of their kingdom before King Sombra took over. King Sombra also returns and threatens to invade the empire again, so Shining Armor and Princess Cadance are sent by Princess Celestia to defend it, projecting a defensive barrier around it.
The Crystal Empire was ruled by King Sombra before its disappearance. It wasn't until after it reappeared that Shining Armor and Cadence had been sent there.
Actually, this is pretty simple: she never did in the first place.
If you look at the source material - mostly the guide book and the Journal of the Two Sisters, you will notice that it never states Cadence was in the Crystal Empire back before it disappearance. At that time, another ruler was in charge, and that was Princess Amore. While this may cause understandable confusion, Princess Amore and Princess Mi Amore Cadenza aren't the same pony at all.
It was only after the reappearance of the Empire that Cadence was sent there because "reasons" and after helping in the defeat of Sombra was accepted as the new ruler. The whereabouts of the original Princess Amore are instead never clearly stated in the show.
The comics may give some further details in the mater - that is, if you are willing to consider them canon (once again, afaik they should be canon unless stated otherwise, but that is up to you to decide).
From the Sombra "Fiend-ship is Magic" comic we know that Princess Amore was turned into stone by Sombra himself and then spitted into pieces that were scattered across the land (to the point that not even Sombra longer knows were they ended up).
Later, the Sombra's return comic arc completes the story of Sombra to the point he is actually reformed (wiping clean any hope of him appearing in the main show in the return). At the end of the arc, he leaves alongside Radiant Hope and goes on a journey to retrieve the lost pieces of Princess Amore statue, hoping to be able to restore her to normal somehow. Anyway, what is really interesting is that in multiple occasions during the arc, Sombra seems to indicate that Cadence is pretty similar to the original Princess Amore. Given that some of side material also states that Amore parents are unknown (she was found by Celestia, and "adopted") some believe that Cadence is indeed intended to be the original Princess Amore reborn somehow (which may explain the reasoning behind the alleged "No filly/before alicorn Cadence stories" veto some says was given to the comic writers) . Sadly, until further details are given, this is only fan speculation and should be treated as such (Personally, I would love to see an appearance of Radiant Hope and Sombra in the main show, but I fear the hopes are slim).
Her parents were the rulers of the Crystal Empire before it had vanished. Cadence's father was the king of the crystal empire (a alicorn too ). He married a peguses so she was a peguses. Her father died in a war against evil spirits. He put a spell to protect his wife and child. So Cadence and her mother were frozen in crystal while King Sombra's rule. So after he was banished, and after a 1000 years the queen and her daughter broke out of the crystal and left Cadence on a path so a earth pony couple will find her. Then she died. So that probably means cadence is about a 1000 years old.